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Bioinformatics Advance Access originally published online on August 12, 2007
Bioinformatics 2007 23(20):2686-2691; doi:10.1093/bioinformatics/btm399
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment

Thomas Tang 1,2,*, Nicolas François 1,4, Annie Glatigny 1, Nicolas Agier 1, Marie-Hélène Mucchielli 1,2, Lawrence Aggerbeck 1 and Hervé Delacroix 1,3

1Centre de Génétique Moléculaire, CNRS UPR2167 and Gif/Orsay DNA MicroArray Platform (GODMAP), 91190 Gif-sur-Yvette, 2Université Pierre et Marie Curie - Paris 6, 75005 Paris, 3Université Paris-Sud - Paris 11, 91405 Orsay, France and 4Department of ARTEMIS, INT, GET, Evry, F-91000

*To whom correspondence should be addressed.


  Abstract

Motivation: Two-colour microarrays are widely used to perform transcriptome analysis. In most cases, it appears that the ‘red’ and ‘green’ images resulting from the scan of a microarray slide are slightly shifted one with respect to the other. To increase the robustness of the measurement of the fluorescent emission intensities, multiple acquisitions with the same or different PMT gains can be used. In these cases, a systematic correction of image shift is required.

Results: To accurately detect this shift, we first developed an approach using cross-correlation. Second, we evaluated the most appropriate interpolation method to be used to derive the registered image. Then, we quantified the effects of image shifts on spot quality, using two different quality estimators. Finally, we measured the benefits associated with a systematic image registration. In this study, we demonstrate that registering the two images prior to data extraction provides a more reliable estimate of the two colours’ ratio and thus increases the accuracy of measurements of variations in gene expression.

Availability: http://bioinfome.cgm.cnrs-gif.fr/

Contact: tang{at}cgm.cnrs-gif.fr

Associate Editor: David Rocke

Received on June 13, 2007; revised on July 26, 2007; accepted on August 2, 2007

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